Transcriptome Sequencing and Analysis of Oat Nuclear Sterile Stamens

doi:10.11733/j.issn.1007-0435.2014.02.022

›› 2014, Vol. 22 ›› Issue (2): 352-358.DOI: 10.11733/j.issn.1007-0435.2014.02.022

Previous Articles Next Articles

Transcriptome Sequencing and Analysis of Oat Nuclear Sterile Stamens

ZHANG Li-jun¹, LIU Long-long¹, QIAO Zhi-jun¹, MA Ming-chuan¹, ZHOU Jian-ping¹, FAN Yin-yan², CUI Lin¹

1. Crop Germplasm Resources Research Institute, Shanxi Academy of Agricultural Sciences; Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, China, Taiyuan, Shanxi Province 030031, China;
2. The Animal Husbandry and Veterinary Research Institute, Shanxi Academy of Agricultural Sciences, Taiyuan, Shanxi Province 030031, China

Received:2013-06-17 Revised:2013-09-01 Online:2014-04-15 Published:2014-04-21

燕麦核不育雄蕊转录组测序及分析

张丽君¹, 刘龙龙¹, 乔治军¹, 马名川¹, 周建萍¹, 范银燕², 崔林¹

1. 山西省农业科学院农作物品种资源研究所农业部黄土高原作物基因资源与种质创制重点实验室, 山西太原 030031;
2. 山西省农业科学院畜牧兽医研究所, 山西太原 030031

通讯作者: 崔林
作者简介:张丽君（1981-），女，河北行唐人，博士，助研，主要从事燕麦遗传育种研究，E-mail：lijun.zhang911@163.com；刘龙龙（1978-），男，山西垣曲人，硕士，助研，主要从事燕麦遗传育种研究，E-mail：lllong781211@sina.com
基金资助:
山西省农科院博士基金项目（YBSJJ209）；国家燕麦荞麦产业技术体系（CARS-08-A-1）资助

Abstract

Abstract: By constructing transcriptome sequencing library of oat near-isogenic lines, Illumina RNA-seq pair terminal sequencing and bioinformatics analysis were done in order to understand the stamen growth process and gene regulation of pollen development. The raw data of 23.13 Gb and the valid data of 20.61 Gb were obtained. The unigene of about 95.95 Mb, contig of 716 nt and N50 of 1.07 kb were obtained through de novo splicing. The results of transcript notes showed that 82992 transcript sequences had homology alignment information; COG and GO functional classification tool divided annotated transcript sequence into 25 and 56 functional categories. Through the comparison of transcript sequences and expression levels between two tested materials, the increased expression quantities of 3643 sequences during the process of stamen development were preliminarily confirmed. The expression quantities of 50 sequences increased more than 10 times, whereas the expression quantities of 12312 sequences decreased and the expression quantities 2041 sequences reduced more than 10 times.

Key words: Oat, Stamen, RNA-seq, Bioinformatics analysis

摘要： 以重组自交构建的燕麦（Avena L.）近等基因系为研究对象，通过构建转录组测序文库并进行Illumina RNA-seq双端测序及生物信息学分析，了解雄蕊生长发育过程，特别是花粉发育基因调控过程。共获得原始数据23.13 Gb，有效数据20.61 Gb。通过 de novo拼接，获得的 unigene 总长度约为 95.95 Mb，均contig长度为716 nt，N50长度为1.07 kb。转录物注释结果显示，82992条转录物序列具有同源比对信息，COG和GO 功能分类工具分别将已注释转录物序列划分为 25个和56 个功能类别。通过对2个材料间转录物序列及表达水平比较，初步确定在雄蕊形成过程中3643条序列表达量上调，50条序列表达量上调10倍以上；12312 条序列表达量下调，2041条序列表达量下调10倍以上。

关键词: 燕麦, 雄蕊, RNA-seq, 生物信息学分析

CLC Number:

ZHANG Li-jun, LIU Long-long, QIAO Zhi-jun, MA Ming-chuan, ZHOU Jian-ping, FAN Yin-yan, CUI Lin. Transcriptome Sequencing and Analysis of Oat Nuclear Sterile Stamens[J]. , 2014, 22(2): 352-358.

张丽君, 刘龙龙, 乔治军, 马名川, 周建萍, 范银燕, 崔林. 燕麦核不育雄蕊转录组测序及分析[J]. , 2014, 22(2): 352-358.

0
/ / Recommend

Add to citation manager EndNote|Ris|BibTeX

URL: https://manu40.magtech.com.cn/Jweb_cdxb/EN/10.11733/j.issn.1007-0435.2014.02.022

https://manu40.magtech.com.cn/Jweb_cdxb/EN/Y2014/V22/I2/352

References

[1] 崔林, 刘龙龙. 中国燕麦品种资源的研究[J]. 现代农业科学, 2009, 16(11)：120-123
[2] 魏利斌, 苗红梅, 张海洋. 芝麻发育转录组分析[J]. 中国农业科学, 2012, 45(7)：1246-1256
[3] Jiao Y P, Zhao H N, Ren L H, et al. Genome-wide genetic changes during modern breeding of maize [J]. Nature Genetics,2012,44(7):812-815
[4] Zheng L Y, Guo X S, He B, et al. Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor) [J]. Genome Biology,2011,12(11):R114
[5] Ashelford K, Eriksson M E, Allen C M, et al. Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis [J]. Genome Biology,2011,12(3):1186-1198
[6] Haun W J, Hyten D L, Xu W W, et al. The composition and origins of genomic variation among individuals of the soybean reference cultivar Williams82 [J]. Plant Physiology,2011,155(2):645-655
[7] Ouyang B, Yang T, Li H X, et al. Identification of early salt stress response genes in tomato root by suppression subtractive hybridization and microarray analysis[J].Journal of Experimental Botany,2007,58(3):507-520
[8] Xiao K, Bai G H, Carver B F. Nylon filter arrays reveal differential expression of expressed sequence tags in wheat roots under aluminum stress [J]. Journal of Integrative Plant Biology,2005,47(7):839-848
[9] Rabbani M A, Maruyama K, Abe H, et al. Monitoring expression profiles of rice genes under cold, drought and high-salinity stresses and abscisic acid application using cDNA microarry and RNA gel-blot analyses [J]. Plant Physiology, 2003,133(4):1755-1767
[10] Lin M Y ,Pedrosa E, Shah A, et al. RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric Disorders [J]. PLoS One,2011,6(9):e23356
[11] Schena M, Shalon D, Heller R, et al. Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes [J]. Proceedings of the National Academy of Sciences of the USA,1996,93(20):10614-10619
[12] Sultan M, Schulz M H, Richard H, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome [J]. Science,2008,321(5891):956-960
[13] Wang E T, Sandberg R, Luo S, et al. Alternative isoform regulation in human tissue transcriptomes [J]. Nature,2008,456(7221):470-476
[14] Birzele F, Schaub J, Rust W, et al. Into the unknown: Expression profiling without genome sequence information in CHO by next generation sequencing [J]. Nucleic Acids Research,2010,38(12):3999-4010
[15] Peng Z Y, Cheng Y B, Tan B C, et al. Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome [J]. Nature Biotechnology,2012,30(3):253-260
[16] Till K Pellny, Alison Lovegrove, Jackie Freeman, et al. Cell walls of developing wheat starchy endosperm: Comparison of composition and RNA-seq transcriptome [J].Plant Physiology February,2012,158(2):612-627
[17] Li Y, Luo H M, Sun C, et al. EST analysis reveals putative genes involved in glycyrrhizin biosynthesis[J]. BMC Genomics,2010,11:R268
[18] Filichkin S A, Priest H D, Givan S A, et al. Genome-wide mapping of alternative splicing in Arabidopsis thaliana [J]. Genome Research,2010,20(1):45-58
[19] Severin A J, Woody J L, Bolon Y T, et al. RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome [J]. BMC Plant Biology,2010,10:R160
[20] Xu Hong, Gao Yi, Wang Jianbo. Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-seq technique [J]. PloS One,2012,7(2):e30646
[21] 徐青,秦恳,张炎,等.不育枸杞花药营养物质代谢与花粉败育的关系[J]. 安徽农业科学,2009,37(3):15566-15569
[22] 徐晓峰. 拟南芥NLC基因特异调控花粉外壁内层发育及花粉壁基因网络关系[D].上海：上海师范大学, 2012:35
[23] Zhang Z B, Zhu J, Gao J F, et al. Transcription factor AtMYB103 is required for anther development by regulating tapetum development,callose dissolution and exine formation in Arabidopsis [J].The Plant Journal,2007,52(3):528-538
[24] Dong X, Hong Z, Sivaramakrishnan M, et al. Callose synthase (CalS5) is required for exine formation during microgametogenesis and for pollen viability in Arabidopsis[J]. The Plant Journal,2005,42(3):315-328
[25] Cao B H, Huang Z Y, Chen G J, et al. Restoring pollen fertility in transgenic male-sterile eggplant by Cre/loxp-mediated site-specific recombination system [J].Genetics and Molecular Biology,2010,33(2)：298-307
[26] Toppino L, Kooiker M, Lindner M, et al. Reversible male sterility in eggplant (Solanum melongena L.) by artificial microRNA-mediated silencing of general transcription factor genes [J]. Plant Biotechnology Journal,2011,9(6):684-692

Transcriptome Sequencing and Analysis of Oat Nuclear Sterile Stamens

燕麦核不育雄蕊转录组测序及分析

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	SONG Ci, HUANG Xiao-tao, SHI Guo-xi, ZHOU Hua-kun, WANG Fang-ping, YAO Bu-qing. Effects of Sowing Dates on the Growth and Forage Quality of Oat on the Qinghai-Tibet Plateau [J]. Acta Agrestia Sinica, 2021, 29(S1): 121-127.
[2]	WU Hai-yan, QU Zhen, LIU Zhao-ming, LABA Dun-zhu, TONGSANG Cuo-mu, QU Ni, NIMA zhuo-ga, MA Yu-shou. Comparative study on Production Performance of Oat Varieties Based on Principal Component Analysis [J]. Acta Agrestia Sinica, 2021, 29(9): 1967-1973.
[3]	PAN Xin-yi, SHI Kun, GONG Pan, WEI Bao, WU Xin-ming, WANG Zan. Transcriptomic Analysis of Anthocyanin Synthesis in Alfalfa [J]. Acta Agrestia Sinica, 2021, 29(5): 866-875.
[4]	TONG Yong-shang, YU Xiao-jun, XU Chang-lin, WANG Peng-bin, SONG Jian-chao, LI Zhen, LI Ying. Effects of Sowing Date on Forage Yield and Quality of Seven Oat Varieties in Tianzhu Alpine Region [J]. Acta Agrestia Sinica, 2021, 29(5): 1094-1106.
[5]	LIANG Guo-ling, LIU Wen-hui, MA Xiang. Phenotypic Diversity of the Panicle Among 590 Covered Oats Germplasm Resources in Apline of Qinghai-Tibet Plateau [J]. Acta Agrestia Sinica, 2021, 29(3): 495-503.
[6]	LIU Bei, SONG Yu-mei, SUN-ming, MAO Pei-sheng. Physiological Responses of Mitochondrial AsA-GSH Cycle to Imbibition of Deteriated Oat Seeds [J]. Acta Agrestia Sinica, 2021, 29(2): 211-219.
[7]	JIA Zhi-feng, MA Xiang, JU Ze-liang, LIU Kai-qiang, ZHAO Gui-qin. Effects of Nitrogen Application Rate and Sowing Rate on Photosynthetic Characteristics,Phytohormone Content and Grain Yield of Oat [J]. Acta Agrestia Sinica, 2021, 29(2): 293-302.
[8]	LI Wen, WEI Ting-hu, Abaodi, Yongcuobazhan, Cairentaci, ZHOU Yu-hai, LI Wen-hao, GUO Wei-xing, ZHANG Yan-ping. Effects of Reduction of Chemical Fertilizer and Organic Manure Supplement on Oat Nutrient Quality and Soil Nutrient in Alpine Cold Region [J]. Acta Agrestia Sinica, 2021, 29(12): 2878-2886.
[9]	WANG Xue, LIU Xiao-jing, ZHAO Ya-jiao, WANG Jing. Effects of Alfalfa/Oat Intercropping on Carbon and Nitrogen Metabolism and Matter Accumulation of Oat [J]. Acta Agrestia Sinica, 2021, 29(10): 2258-2264.
[10]	ZHOU Lei, WANG Lu, ZHAO Bao-ping, MI Jun-zhen, WANG Feng-wu, LIU Jing-hui, ZHANG Dan, LIU Ye-kun. Effect of Different Sowing Date and Cutting Time on Yield and Quality of Forage Oat in Agro-pastoral Ecotone of Northern China [J]. Acta Agrestia Sinica, 2021, 29(10): 2355-2363.
[11]	FU Dong-qing, WANG Yan-chao, SONG Lei, WANG Xu-zhe, ZHANG Fan-fan, MA Chun-hui. Effects of Nitrogen Application Rate and Planting Density on Production Performance of Early Maturing Forage Oat in Shihezi,Xinjiang [J]. Acta Agrestia Sinica, 2021, 29(10): 2364-2371.
[12]	JIA Zhi-feng, MA Xiang, JU Ze-liang, LIU Kai-qiang, ZHAO Gui-qin. Effects of Nitrogen Fertilizer and Plant Density on Oat Leaf Senescence Characteristics and Cell Structure [J]. Acta Agrestia Sinica, 2021, 29(1): 80-87.
[13]	SUN Hao-yang, ZHAO Gui-qin, ZHANG Jian-gui, LI Xin, YANG Yan-shan, CHAI Ji-kuan, ZENG Liang, JIAO Run-an, JIN Xiao-wen, LI Rong, GONG Wen-long. Incidence of Oat Powdery Mildew and Pathogen Identification in the Main Oat Production Areas of Gansu Province [J]. Acta Agrestia Sinica, 2020, 28(6): 1535-1543.
[14]	LIU Kai-qiang, LIU Wen-hui, JIA Zhi-feng, MA Xiang, LIANG Guo-ling. Effects of Water Stress on Organ Growth and Water Use Efficiency of Avena sativa ‘Qingyan No. 1’ [J]. Acta Agrestia Sinica, 2020, 28(6): 1552-1562.
[15]	HAO Shuang-nan, QIN Jie, LIU Pan-feng, YANG Wu-de, ZHANG Mei-jun, FENG Mei-chen, WANG Chao, SONG Xiao-yan. Effects of Exogenous Selenium on Stem Characteristics and Lodging Resistance of Oat [J]. Acta Agrestia Sinica, 2020, 28(6): 1572-1579.